GSE Subsidy Elimination Act of 2011 - Amends the Housing and Community Development Act of 1992 to require the Director of the Federal Housing Finance Agency to require the Federal National Mortgage Association (Fannie Mae) and the Federal Home Loan Mortgage Corporation (Freddie Mac) (government-sponsored enterprises or GSEs) to charge a guarantee fee in connection with any guarantee of the timely payment of principal and interest on securities, notes, and other obligations based on or backed by mortgages on residential real properties designed principally for occupancy of from one to four families. Requires the fee to be set at an amount that appropriately reflects risk of loss as well as the cost of capital allocated to similar assets held by other fully private regulated financial institutions.
Directs the Director to require each GSE to increase its guarantee fee gradually over two years in a manner sufficient to comply with this Act.